SAXSdb — 4wma

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Xyloside xylosyltransferase 1

Mus musculus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 2 其他Polymer 1	Coagulation factor IX × 1 （P00740） alpha-D-xylopyranose-(1-3)-beta-D-glucopyranose × 1 MANGANESE (II) ION × 1 URIDINE-5'-DIPHOSPHATE-GLUCOSE × 1 SULFATE ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	XXLT1_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–306； UniProt 87–392

Coagulation factor IX

Homo sapiens

UniProt P00740

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 2 其他Polymer 1	Xyloside xylosyltransferase 1 × 1 （Q3U4G3） alpha-D-xylopyranose-(1-3)-beta-D-glucopyranose × 1 MANGANESE (II) ION × 1 URIDINE-5'-DIPHOSPHATE-GLUCOSE × 1 SULFATE ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	FA9_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 4–42； UniProt 92–130

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4wma
Deposition date deposition_date	2014-10-08
Structure title title	Crystal structure of mouse Xyloside xylosyltransferase 1 complexed with manganese,acceptor ligand and UDP-Glucose
Keywords keywords	glycosyltransferase, transferase-protein binding complex; transferase/protein binding
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

4wma__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4wma__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4wma__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	20.81 Å
Rg (electron density)	19.78 Å
Total Rg	20.63 Å
Atom count	2765
Residues	334
Excluded volume	49069 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4wma__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Xyloside xylosyltransferase 1
Molecular weight formula_weight	35295.5 kDa
EC 编号 ec_number	2.4.2.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2905

SLEGGVVVPVDYHLLMMFTKAEHNAPLQAKARVALSSLLRLAKFEAHEVLNLHFVSEEASREVAKALLRELLPPAAGFKCKVIFHDVAVLTDKLFPVVEAMQKYFSAGSGTYYSDSIFFLSVAMHQIMPKEIPRIIQLDLDLKYKTNIRELFEEFDNFLPGAVIGIAREMQPVYRHTFWQFRHENPKTRVGDPPPEGLPGFNSGVMLLNLEAMRQSPLYSHLLEPSWVQQLADKYHFRGHLGDQDFFTMIGMEHPELFHVLDCTWNRQLCTWWRDHGYSDVFQAYFRCEGHVKIYHGNCNTPIPED

Source Source

Source organism organism	Mus musculus
Common name common_name	Mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Coagulation factor IX
Molecular weight formula_weight	5710.2 kDa
EC 编号 ec_number	3.4.21.22
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MDIVDGDQCESNPCLNGGSCKDDINSYECWCPFGFEGKNCELLEHHHHHH

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 branched

Description description	alpha-D-xylopyranose-(1-3)-beta-D-glucopyranose
Molecular weight formula_weight	312.3 kDa
Source method src_method	man
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	URIDINE-5'-DIPHOSPHATE-GLUCOSE
Molecular weight formula_weight	566.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	135

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6. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d4wmad_
Class class	g — Small proteins
Fold Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamily	g.3.11 — EGF/Laminin
Family Family family	g.3.11.1 — EGF-type module

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Unit-cell length a length_a	90.028 Å
Unit-cell length b length_b	90.028 Å
Unit-cell length c length_c	43.136 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	3

Space group space_group	P 3
Space-group number int_tables_number	143
Crystal system crystal_system	—

Resolution resolution	1.620 Å
Low-resolution limit resolution_low	77.970 Å
R factor r_factor	0.2203
R_work r_work	0.2191
R_free r_free	0.2425

Crystal structure of mouse Xyloside xylosyltransferase 1 complexed with manganese,acceptor ligand and UDP-Glucose

1. Protein Identity and Related Structures Protein Identity & Related Structures

Xyloside xylosyltransferase 1

State in the Current Structure

Other States of the Same Protein in the Database

Coagulation factor IX

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4wma__assembly_1__model_1

4wma__assembly_1__model_1 | I(q)

4wma__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 branched

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

7. Citations (1)

Crystal structure of mouse Xyloside xylosyltransferase 1 complexed with manganese,acceptor ligand and UDP-Glucose

1. Protein Identity and Related Structures Protein Identity & Related Structures

Xyloside xylosyltransferase 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Coagulation factor IX

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4wma__assembly_1__model_1

4wma__assembly_1__model_1 | I(q)

4wma__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 branched

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

7. Citations (1)